This is really amazing – I hope you succeed to help boost the popularity of MonoBrick firmware…

Isolate timer in even higher priority thread to improve accuracy?

I already think that your approach with the hight priority thread seems good enough (if I understand correctly)

How to debug this on the brick? Xamarin seems to have a bug with mono on windows currently.

Log values to an array and when done write these to a file to plot in matlab. This way you only spend time on “saving” values to the array. It would be nice to debug over a WiFi connection – but for a real-time system it does not make sense. So from your point of view it does not matter if debugging is working or not. Also make sure that when running tests use a release build to get the best performance.